Microbiome Data Visualization
Get a public 16S-demo dataset
Using dietswap from microbiome package
phyloseq-class experiment-level object
otu_table() OTU Table: [ 130 taxa and 222 samples ]
sample_data() Sample Data: [ 222 samples by 8 sample variables ]
tax_table() Taxonomy Table: [ 130 taxa by 3 taxonomic ranks ]Explore variables and missing values
# A tibble: 14 × 4
variable type unique p_zeros
<chr> <chr> <int> <dbl>
1 sample_id character 28860 0
2 otu character 130 0
3 sample character 222 0
4 abundance numeric 1268 20.6
5 subject factor 38 0
6 sex factor 2 0
7 nationality factor 2 0
8 group factor 3 0
9 timepoint integer 6 0
10 timepoint.within.group integer 2 0
11 bmi_group factor 3 0
12 phylum character 8 0
13 family character 22 0
14 genus character 130 0 Frequency distributions for categoric variables
sex frequency percentage cumulative_perc
1 male 15600 54.05 54.05
2 female 13260 45.95 100.00
nationality frequency percentage cumulative_perc
1 AAM 15990 55.41 55.41
2 AFR 12870 44.59 100.00
group frequency percentage cumulative_perc
1 ED 9750 33.78 33.78
2 HE 9750 33.78 67.56
3 DI 9360 32.43 100.00
bmi_group frequency percentage cumulative_perc
1 obese 11700 40.54 40.54
2 overweight 9880 34.23 74.77
3 lean 7280 25.23 100.00[1] "Variables processed: sex, nationality, group, bmi_group"Correlation of numeric varaiables
Variable sex
1 sex 1.00
2 abundance 0.00
3 timepoint -0.01Boxplot
Density histogram
Predictive model performance
Gain and lift performance curve
Dataset: heart_disease from funModeling
Population Gain Lift Score.Point
1 10 20.86 2.09 0.8185793
2 20 35.97 1.80 0.6967124
3 30 48.92 1.63 0.5657817
4 40 61.15 1.53 0.4901940
5 50 69.06 1.38 0.4033640
6 60 78.42 1.31 0.3344170
7 70 87.77 1.25 0.2939878
8 80 92.09 1.15 0.2473671
9 90 96.40 1.07 0.1980453
10 100 100.00 1.00 0.1195511Coordinate plot: Profile mean clusters
cyl mpg disp hp drat wt qsec vs am gear carb
1 4 26.0 108.0 91.0 4.080 2.200 18.90 1 1 4 2.0
2 6 19.7 167.6 110.0 3.900 3.210 18.30 1 0 4 4.0
3 8 15.2 350.5 192.5 3.120 3.760 17.18 0 0 3 3.5
4 All_Data 19.2 196.3 123.0 3.695 3.325 17.71 0 0 4 2.0Snakemake workflow
Heatmaps
Using qiime2R
Using ggplot
Bray-Curtis
Jaccard
Bray-Curtis and Jaccard
Using microViz
Heatmap without sample annotation
Heatmap with sample annotation
Jitter plots
Line plots
PCoA ordination
References
[1]
Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C.,
Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated
bioinformatics and visualization pipeline for microbiome data analysis.
BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4
Appendix
Project main tree
.
├── LICENSE
├── README.md
├── Rplots.pdf
├── config
│  └── config.yml
├── css
├── dags
│  ├── rulegraph.png
│  └── rulegraph.svg
├── data
│  ├── feature_table.qza
│  ├── features.csv
│  ├── metadata.csv
│  ├── processed_data.rda
│  ├── processed_objects.rda
│  ├── rooted_tree.qza
│  ├── sample_metadata.tsv
│  ├── shannon.csv
│  ├── shannon_vector.qza
│  ├── taxonomy.csv
│  ├── taxonomy.qza
│  └── unweighted_unifrac_pcoa.qza
├── figures
│  ├── bmi_group.jpeg
│  ├── boxplot-1.png
│  ├── boxplot-2.png
│  ├── bray-1.png
│  ├── bray_jcard-1.png
│  ├── coord-1.png
│  ├── freq_catvars-1.png
│  ├── freq_catvars-2.png
│  ├── freq_catvars-3.png
│  ├── freq_catvars-4.png
│  ├── ggplot_heatmap.png
│  ├── ggplot_heatmap.svg
│  ├── glm-1.png
│  ├── group.jpeg
│  ├── histdens-1.png
│  ├── histdens-2.png
│  ├── jaccard-1.png
│  ├── microviz_heatmap.png
│  ├── microviz_heatmap.svg
│  ├── microvizhtmp-1.png
│  ├── micrvizannothtmp-1.png
│  ├── nationality.jpeg
│  ├── q2r_barplot.png
│  ├── q2r_barplot.svg
│  ├── q2r_heatmap.png
│  ├── q2r_heatmap.svg
│  ├── q2r_jitterplot.png
│  ├── q2r_jitterplot.svg
│  ├── q2r_lineplot.png
│  ├── q2r_lineplot.svg
│  ├── q2r_pcoa.png
│  ├── q2r_pcoa.svg
│  ├── sex.jpeg
│  ├── taxahtmp-1.png
│  ├── unnamed-chunk-1-1.png
│  ├── unnamed-chunk-2-1.png
│  ├── unnamed-chunk-3-1.png
│  ├── unnamed-chunk-4-1.png
│  ├── unnamed-chunk-5-1.png
│  ├── unnamed-chunk-6-1.png
│  └── unnamed-chunk-7-1.png
├── images
│  ├── bkgd.png
│  ├── coders.png
│  ├── ml.png
│  ├── smkreport
│  │  └── screenshot.png
│  └── vizcover.png
├── imap-data-visualization.Rproj
├── index.Rmd
├── library
│  ├── apa.csl
│  ├── export.bib
│  ├── imap.bib
│  ├── packages.bib
│  └── references.bib
├── report.html
├── results
│  └── project_tree.txt
├── styles.css
└── workflow
├── Snakefile
├── envs
│  └── environment.yml
├── report
│  ├── barplot.rst
│  ├── boxplots.rst
│  ├── hcluster.rst
│  ├── heatmap.rst
│  ├── jitterplot.rst
│  ├── lineplot.rst
│  ├── nmds.rst
│  ├── pcaordi.rst
│  ├── pcoa.rst
│  ├── scatter.rst
│  ├── venndiagram.rst
│  ├── volcano.rst
│  └── workflow.rst
├── rules
│  ├── barplot.smk
│  ├── gh_pages.smk
│  ├── heatmap.smk
│  ├── jitter.smk
│  ├── lineplot.smk
│  ├── pcoa.smk
│  ├── processed_data.smk
│  ├── project_tree.smk
│  ├── rulegraph.smk
│  ├── smk_report.smk
│  ├── venn.smk
│  └── visual_types.smk
└── scripts
├── README.md
├── alpha.R
├── barplot.R
├── build_bs4_book.bash
├── common.R
├── custom_theme.R
├── heatmap.R
├── jitterplot.R
├── lefse.R
├── lineplot.R
├── pcoa.R
├── processed_data.R
├── qiime2R.R
├── qiime2csv.R
├── rarefy.R
├── read_matrix.R
├── render.R
├── rules_dag.sh
├── smk_html_report.sh
├── tree.sh
└── volcanoplot.R
14 directories, 122 files
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